[2024-01-24 13:17:27,061] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:27,063] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:27,063] [INFO] DQC Reference Directory: /var/lib/cwl/stg25cadde3-0936-4846-8091-329268185017/dqc_reference
[2024-01-24 13:17:28,282] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:28,283] [INFO] Task started: Prodigal
[2024-01-24 13:17:28,283] [INFO] Running command: gunzip -c /var/lib/cwl/stg576ecf6e-e4f7-4dc7-9276-b4e618204731/GCF_000325665.1_ASM32566v1_genomic.fna.gz | prodigal -d GCF_000325665.1_ASM32566v1_genomic.fna/cds.fna -a GCF_000325665.1_ASM32566v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:32,427] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:32,428] [INFO] Task started: HMMsearch
[2024-01-24 13:17:32,428] [INFO] Running command: hmmsearch --tblout GCF_000325665.1_ASM32566v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25cadde3-0936-4846-8091-329268185017/dqc_reference/reference_markers.hmm GCF_000325665.1_ASM32566v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:32,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:32,655] [INFO] Found 6/6 markers.
[2024-01-24 13:17:32,678] [INFO] Query marker FASTA was written to GCF_000325665.1_ASM32566v1_genomic.fna/markers.fasta
[2024-01-24 13:17:32,679] [INFO] Task started: Blastn
[2024-01-24 13:17:32,679] [INFO] Running command: blastn -query GCF_000325665.1_ASM32566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25cadde3-0936-4846-8091-329268185017/dqc_reference/reference_markers.fasta -out GCF_000325665.1_ASM32566v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:33,262] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:33,266] [INFO] Selected 11 target genomes.
[2024-01-24 13:17:33,267] [INFO] Target genome list was writen to GCF_000325665.1_ASM32566v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:33,293] [INFO] Task started: fastANI
[2024-01-24 13:17:33,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg576ecf6e-e4f7-4dc7-9276-b4e618204731/GCF_000325665.1_ASM32566v1_genomic.fna.gz --refList GCF_000325665.1_ASM32566v1_genomic.fna/target_genomes.txt --output GCF_000325665.1_ASM32566v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:41,737] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:41,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25cadde3-0936-4846-8091-329268185017/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:41,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25cadde3-0936-4846-8091-329268185017/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:41,750] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:41,750] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:41,750] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Brachyspira pilosicoli	strain=P43/6/78	GCA_000325665.1	52584	52584	type	True	100.0	850	851	95	conclusive
Brachyspira intermedia	strain=PWS/A	GCA_000223215.1	84377	84377	type	True	81.8197	556	851	95	below_threshold
Brachyspira suanatina	strain=AN4859/03	GCA_001049755.1	381802	381802	type	True	81.6291	556	851	95	below_threshold
Brachyspira hyodysenteriae	strain=B78	GCA_000383255.1	159	159	type	True	81.5924	543	851	95	below_threshold
Brachyspira hyodysenteriae	strain=B78	GCA_001013005.1	159	159	type	True	81.5403	551	851	95	below_threshold
Brachyspira hyodysenteriae	strain=B-78	GCA_001676785.2	159	159	type	True	81.5064	543	851	95	below_threshold
Brachyspira murdochii	strain=DSM 12563	GCA_000092845.1	84378	84378	type	True	80.9012	532	851	95	below_threshold
Brachyspira alvinipulli	strain=ATCC 51933	GCA_000518245.1	84379	84379	type	True	80.8898	543	851	95	below_threshold
Brachyspira innocens	strain=B256	GCA_000384655.1	13264	13264	type	True	80.8895	559	851	95	below_threshold
Brachyspira hampsonii	strain=NSH-16	GCA_002214805.1	1287055	1287055	type	True	80.7628	544	851	95	below_threshold
Brachyspira hampsonii	strain=NSH-16	GCA_001746225.1	1287055	1287055	type	True	80.7223	526	851	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:41,753] [INFO] DFAST Taxonomy check result was written to GCF_000325665.1_ASM32566v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:41,753] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:41,754] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:41,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25cadde3-0936-4846-8091-329268185017/dqc_reference/checkm_data
[2024-01-24 13:17:41,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:41,786] [INFO] Task started: CheckM
[2024-01-24 13:17:41,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000325665.1_ASM32566v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000325665.1_ASM32566v1_genomic.fna/checkm_input GCF_000325665.1_ASM32566v1_genomic.fna/checkm_result
[2024-01-24 13:18:01,939] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:01,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:01,954] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:01,954] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:01,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000325665.1_ASM32566v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:01,955] [INFO] Task started: Blastn
[2024-01-24 13:18:01,955] [INFO] Running command: blastn -query GCF_000325665.1_ASM32566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25cadde3-0936-4846-8091-329268185017/dqc_reference/reference_markers_gtdb.fasta -out GCF_000325665.1_ASM32566v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:02,802] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:02,805] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:02,805] [INFO] Target genome list was writen to GCF_000325665.1_ASM32566v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:02,836] [INFO] Task started: fastANI
[2024-01-24 13:18:02,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg576ecf6e-e4f7-4dc7-9276-b4e618204731/GCF_000325665.1_ASM32566v1_genomic.fna.gz --refList GCF_000325665.1_ASM32566v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000325665.1_ASM32566v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:12,125] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:12,134] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:12,135] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000325665.1	s__Brachyspira pilosicoli	100.0	850	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	98.38	97.84	0.95	0.91	19	conclusive
GCF_009755885.1	s__Brachyspira sp009755885	91.78	754	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008016535.1	s__Brachyspira pilosicoli_A	91.643	686	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000223215.1	s__Brachyspira intermedia	81.8014	557	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001049755.1	s__Brachyspira suanatina	81.6413	555	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676785.2	s__Brachyspira hyodysenteriae	81.4446	548	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	99.16	98.93	0.98	0.95	58	-
GCF_000384655.1	s__Brachyspira innocens	80.937	555	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518245.1	s__Brachyspira alvinipulli	80.8781	544	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092845.1	s__Brachyspira murdochii	80.8623	534	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	97.81	96.97	0.94	0.93	3	-
GCF_001746205.1	s__Brachyspira hampsonii_B	80.8459	530	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316195.1	s__Brachyspira hampsonii_C	80.7527	527	851	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	98.70	97.44	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:12,136] [INFO] GTDB search result was written to GCF_000325665.1_ASM32566v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:12,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:12,140] [INFO] DFAST_QC result json was written to GCF_000325665.1_ASM32566v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:12,140] [INFO] DFAST_QC completed!
[2024-01-24 13:18:12,140] [INFO] Total running time: 0h0m45s